Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014672.1 Kokia drynarioides strain JFW-HI SEQ_129711, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 69557
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:12699 original size:42 final size:42
Alignment explanation
Indices: 12533--13064 Score: 239
Period size: 43 Copynumber: 12.8 Consensus size: 42
12523 CCATCCCATT
* * * *
12533 CAATCTCTTACCCTAACCATG-GGGTAGATTG-AAGC--CATT
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAAACATCATC
* * * * *
12572 CAACCTTCTACCCTAACTAGAGGACAGATTG-AAACACCATC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAAACATCATC
* ** * *
12613 CAATCTCTTACCCCGACCATGA-GACAGATTG--AA-GTCATC
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAAACATCATC
*
12652 CAATCTTTTAACCTAACCAGAGGGCAGATTGAAAACATCATC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAAACATCATC
* * * * * * *
12694 TAATCTCTTACCCTGACCATGA-CGTAGATTG--AA-GTCAAC
1 CAATCTTTTACCCTAACCA-GAGGGCAGATTGAAAACATCATC
* *
12733 TAATCTTTTACCCTAACTAGAGGGCAGATT-AAAGACATCATC
1 CAATCTTTTACCCTAACCAGAGGGCAGATTGAAA-ACATCATC
* * * * * **
12775 CAATCTCTTA-CCTCGACCATAGGGCAAATCG--AA-ATTGTC
1 CAATCTTTTACCCT-AACCAGAGGGCAGATTGAAAACATCATC
* * * * * *
12814 CAATCTTTTACCCTAATCCAGATGGTAAATT-AAAGCCACCGTC
1 CAATCTTTTACCCTAA-CCAGAGGGCAGATTGAAA-ACATCATC
* * * * *
12857 CAATCTTTTACCCTAATCCAGAGGGTAAATT-AAAGCCACCGTC
1 CAATCTTTTACCCTAA-CCAGAGGGCAGATTGAAA-ACATCATC
* * ** *
12900 CAATCTTTTACCCTAATCCAGAAGGAAGATT-AAAGTTACCATC
1 CAATCTTTTACCCTAA-CCAGAGGGCAGATTGAAA-ACATCATC
* *
12943 CAATCTTTTACCCTAATCTAGAGGGCAAATTGAAGCAAC--CATC
1 CAATCTTTTACCCTAA-CCAGAGGGCAGATTGAA--AACATCATC
* *
12986 CAATCTTTTACCCTAATCTAGAGGGCAGATT-AAAGTCATCATC
1 CAATCTTTTACCCTAA-CCAGAGGGCAGATTGAAA-ACATCATC
** *
13029 CAATCTCTTGCCCCTAATCCAAAGGGACAGATTGAA
1 CAATCT-TTTACCCTAA-CCAGAGGG-CAGATTGAA
13065 GTTACAACAT
Statistics
Matches: 388, Mismatches: 74, Indels: 55
0.75 0.14 0.11
Matches are distributed among these distances:
38 5 0.01
39 93 0.24
40 20 0.05
41 34 0.09
42 54 0.14
43 156 0.40
44 17 0.04
45 6 0.02
46 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (42 bp):
CAATCTTTTACCCTAACCAGAGGGCAGATTGAAAACATCATC
Found at i:12819 original size:81 final size:82
Alignment explanation
Indices: 12528--13037 Score: 363
Period size: 81 Copynumber: 6.2 Consensus size: 82
12518 TTACACCATC
* * * * * ** * * * *
12528 CCATTCAATCTCTTACCCTAACCATGGGGTAGATTGAAGCCATTCAACCTTCTACCCTAA-CTAG
1 CCATCCAATCTCTTACCCTGACCATAGGGCAAATTGAAATCATCCAATCTTTTACCCTAATCCAG
* *
12592 AGGACAGATTGAA-ACA
66 AGGGCAGATTAAAGACA
* * * * *
12608 CCATCCAATCTCTTACCCCGACCAT-GAGACAGATTGAAGTCATCCAATCTTTTAACCTAA-CCA
1 CCATCCAATCTCTTACCCTGACCATAG-GGCAAATTGAAATCATCCAATCTTTTACCCTAATCCA
12671 GAGGGCAGATTGAAA-ACA
65 GAGGGCAGATT-AAAGACA
* * * * * * * * *
12689 TCATCTAATCTCTTACCCTGACCAT-GACGTAGATTGAAGTCAACTAATCTTTTACCCTAA-CTA
1 CCATCCAATCTCTTACCCTGACCATAG-GGCAAATTGAAATCATCCAATCTTTTACCCTAATCCA
12752 GAGGGCAGATTAAAGACA
65 GAGGGCAGATTAAAGACA
* * **
12770 TCATCCAATCTCTTA-CCTCGACCATAGGGCAAATCGAAATTGTCCAATCTTTTACCCTAATCCA
1 CCATCCAATCTCTTACCCT-GACCATAGGGCAAATTGAAATCATCCAATCTTTTACCCTAATCCA
* * * *
12834 GATGGTAAATTAAAGCCA
65 GAGGGCAGATTAAAGACA
* * * * * *
12852 CCGTCCAATCTTTTACCCTAATCCAGAGGGTAAATT-AAAGCCACCGTCCAATCTTTTACCCTAA
1 CCATCCAATCTCTTACCCTGA-CCATAGGGCAAATTGAAA-TCA---TCCAATCTTTTACCCTAA
* * **
12916 TCCAGAAGGAAGATTAAAGTTA
61 TCCAGAGGGCAGATTAAAGACA
* * * * *
12938 CCATCCAATCTTTTACCCTAATCTAGAGGGCAAATTGAAGCAACCATCCAATCTTTTACCCTAAT
1 CCATCCAATCTCTTACCCTGA-CCATAGGGCAAATTG-A--AATCATCCAATCTTTTACCCTAAT
* *
13003 CTAGAGGGCAGATTAAAGTCA
62 CCAGAGGGCAGATTAAAGACA
*
13024 TCATCCAATCTCTT
1 CCATCCAATCTCTT
13038 GCCCCTAATC
Statistics
Matches: 352, Mismatches: 62, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
79 1 0.00
80 66 0.19
81 116 0.33
82 33 0.09
83 14 0.04
86 116 0.33
88 1 0.00
89 3 0.01
90 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (82 bp):
CCATCCAATCTCTTACCCTGACCATAGGGCAAATTGAAATCATCCAATCTTTTACCCTAATCCAG
AGGGCAGATTAAAGACA
Found at i:12859 original size:43 final size:43
Alignment explanation
Indices: 12812--13054 Score: 299
Period size: 43 Copynumber: 5.6 Consensus size: 43
12802 ATCGAAATTG
* * *
12812 TCCAATCTTTTACCCTAATCCAGATGGTAAATTAAAGCCACCG
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCCACCA
* *
12855 TCCAATCTTTTACCCTAATCCAGAGGGTAAATTAAAGCCACCG
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCCACCA
* **
12898 TCCAATCTTTTACCCTAATCCAGAAGG-AAGATTAAAGTTACCA
1 TCCAATCTTTTACCCTAATCCAGAGGGCAA-ATTAAAGCCACCA
* * *
12941 TCCAATCTTTTACCCTAATCTAGAGGGCAAATTGAAGCAACCA
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCCACCA
* * * *
12984 TCCAATCTTTTACCCTAATCTAGAGGGCAGATTAAAGTCATCA
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCCACCA
** *
13027 TCCAATCTCTTGCCCCTAATCCAAAGGG
1 TCCAATCT-TTTACCCTAATCCAGAGGG
13055 ACAGATTGAA
Statistics
Matches: 178, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
42 2 0.01
43 159 0.89
44 17 0.10
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (43 bp):
TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCCACCA
Found at i:12988 original size:129 final size:131
Alignment explanation
Indices: 12812--13069 Score: 351
Period size: 129 Copynumber: 2.0 Consensus size: 131
12802 ATCGAAATTG
* * * *
12812 TCCAATCTTTTACCCTAATCCAGATGGTAAATTAAAGCCACCGTCCAATCTTTTACCCTAATCCA
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCAACCATCCAATCTTTTACCCTAATCCA
* * *
12877 GAGGGTAAATTAAAGCCACCGTCCAATCT-TTTACCCTAATCCAGAA-GGA-AGATTAAAGTTAC
66 GAGGGCAAATTAAAGCCACCATCCAATCTCTTGACCCTAATCCA-AAGGGACAGATTAAAGTTAC
12939 CA
130 CA
* * *
12941 TCCAATCTTTTACCCTAATCTAGAGGGCAAATTGAAGCAACCATCCAATCTTTTACCCTAATCTA
1 TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCAACCATCCAATCTTTTACCCTAATCCA
* * * * *
13006 GAGGGCAGATTAAAGTCATCATCCAATCTCTTGCCCCTAATCCAAAGGGACAGATTGAAGTTAC
66 GAGGGCAAATTAAAGCCACCATCCAATCTCTTGACCCTAATCCAAAGGGACAGATTAAAGTTAC
13070 AACATCAAAC
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 84 0.76
130 15 0.14
131 12 0.11
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (131 bp):
TCCAATCTTTTACCCTAATCCAGAGGGCAAATTAAAGCAACCATCCAATCTTTTACCCTAATCCA
GAGGGCAAATTAAAGCCACCATCCAATCTCTTGACCCTAATCCAAAGGGACAGATTAAAGTTACC
A
Found at i:15777 original size:89 final size:88
Alignment explanation
Indices: 15682--15881 Score: 274
Period size: 89 Copynumber: 2.2 Consensus size: 88
15672 CCTAGTGATG
* *
15682 GATTTTATCTATGATATTTTTCTGTGTACCACAACCCAGTGGCAAGTTTCACCTGCAAATTTTCG
1 GATTTTATCTATGATATTTTT-TGTGTACCACAACCCAATGGCAAGTTTCACCTGCAAATTTTAG
* *
15747 TTGTGTATCCACAGCATAGTGGCA
65 CTCTGTATCCACAGCATAGTGGCA
* * * * * *
15771 GATTTTATCTGTGATATTTTGTTGTGTACCACAACCTAATGGTAGGTTTCATCTGCGAATTTTAG
1 GATTTTATCTATGATATTTT-TTGTGTACCACAACCCAATGGCAAGTTTCACCTGCAAATTTTAG
*
15836 CTCTGTATCCACAGCCTAGTGGCA
65 CTCTGTATCCACAGCATAGTGGCA
*
15860 GATTTTATCTACGATATTTTTT
1 GATTTTATCTATGATATTTTTT
15882 TTGCGTACCC
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
88 2 0.02
89 94 0.97
90 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (88 bp):
GATTTTATCTATGATATTTTTTGTGTACCACAACCCAATGGCAAGTTTCACCTGCAAATTTTAGC
TCTGTATCCACAGCATAGTGGCA
Found at i:15825 original size:44 final size:45
Alignment explanation
Indices: 15694--15947 Score: 176
Period size: 45 Copynumber: 5.7 Consensus size: 45
15684 TTTTATCTAT
* * * *
15694 GATATTTT-TCTGTGTA-CCACAACCCAGTGGCAAGTTTCACCTGC
1 GATATTTTGT-TGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
* * * * *
15738 -AAATTTTCGTTGTGTATCCACAGCATAGTGGCAGATTTTATCTGT
1 GATATTTT-GTTGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
* * *
15783 GATATTTTGTTGTGTA-CCACAACCTAATGGTAGGTTTCATCTGC
1 GATATTTTGTTGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
* * * * *
15827 GA-ATTTTAGCTCTGTATCCACAGCCTAGTGGCAGATTTTATCTAC
1 GATATTTT-GTTGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
* * * * * * * *
15872 GATATTTTTTTTGCGTACCCACAGCCCAATGGTAGGTTTCATTTAC
1 GATA-TTTTGTTGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
* * * *
15918 GATTTTTTGTAGTGTATCCATAGCCAAGTG
1 GATATTTTGTTGTGTATCCACAGCCTAGTG
15948 ACAGATTTTA
Statistics
Matches: 158, Mismatches: 44, Indels: 15
0.73 0.20 0.07
Matches are distributed among these distances:
43 11 0.07
44 35 0.22
45 72 0.46
46 36 0.23
47 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (45 bp):
GATATTTTGTTGTGTATCCACAGCCTAGTGGCAGGTTTCATCTGC
Found at i:15953 original size:91 final size:89
Alignment explanation
Indices: 15682--15957 Score: 270
Period size: 89 Copynumber: 3.1 Consensus size: 89
15672 CCTAGTGATG
* * * * * * * * *
15682 GATTTTATCTATGATATTTT-TCTGTGTACCACAACCCAGTGGCAAGTTTCACCTGCAAATTTTC
1 GATTTTATCTACGATATTTTGT-TGCGTACCACAACCCAATGGTAGGTTTCATCTACGAATTTTA
*
15746 GTTGTGTATCCACAG-CATAGTGGCA
65 GCTGTGTATCCACAGCCA-AGTGGCA
** * * *
15771 GATTTTATCTGTGATATTTTGTTGTGTACCACAACCTAATGGTAGGTTTCATCTGCGAATTTTAG
1 GATTTTATCTACGATATTTTGTTGCGTACCACAACCCAATGGTAGGTTTCATCTACGAATTTTAG
* *
15836 CTCTGTATCCACAGCCTAGTGGCA
66 CTGTGTATCCACAGCCAAGTGGCA
* * * *
15860 GATTTTATCTACGATATTTTTTTTGCGTACCCACAGCCCAATGGTAGGTTTCATTTACGATTTTT
1 GATTTTATCTACGATA-TTTTGTTGCGTA-CCACAACCCAATGGTAGGTTTCATCTACGAATTTT
* * *
15925 TG-TAGTGTATCCATAGCCAAGTGACA
64 AGCT-GTGTATCCACAGCCAAGTGGCA
15951 GATTTTA
1 GATTTTA
15958 CTGCGAAACT
Statistics
Matches: 157, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
89 88 0.56
90 13 0.08
91 56 0.36
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (89 bp):
GATTTTATCTACGATATTTTGTTGCGTACCACAACCCAATGGTAGGTTTCATCTACGAATTTTAG
CTGTGTATCCACAGCCAAGTGGCA
Found at i:17690 original size:36 final size:36
Alignment explanation
Indices: 17649--17791 Score: 160
Period size: 36 Copynumber: 4.0 Consensus size: 36
17639 TGGCTATTGT
* *
17649 GATAGTAAATGTGTGAGTATGTTATTCATGCCATGG
1 GATAGTAAATATGTGAGTATGTTATTCATGCCATGA
* * * * *
17685 GATAGTAAATATGTGGGTATATTTTTCATGTCATGT
1 GATAGTAAATATGTGAGTATGTTATTCATGCCATGA
* *
17721 GACAGTAAATATGTGAGTATGTTATTCATGCCTTGA
1 GATAGTAAATATGTGAGTATGTTATTCATGCCATGA
* * * * *
17757 GATAGAAAATATATGTGTATGTTATTTATGTCATG
1 GATAGTAAATATGTGAGTATGTTATTCATGCCATG
17792 TGACAGTGAA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 87 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (36 bp):
GATAGTAAATATGTGAGTATGTTATTCATGCCATGA
Found at i:17728 original size:72 final size:72
Alignment explanation
Indices: 17646--17804 Score: 221
Period size: 72 Copynumber: 2.2 Consensus size: 72
17636 TGATGGCTAT
* * * * *
17646 TGTGATAGTAAATGTGTGAGTATGTTATTCATGCCATGGGATAGTAAATATGTGGGTATATT-TT
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGATAGAAAATATATGGGTATATTATT
17710 TCATGTCA
66 T-ATGTCA
* * *
17718 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCTTGAGATAGAAAATATATGTGTATGTTATT
1 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGATAGAAAATATATGGGTATATTATT
17783 TATGTCA
66 TATGTCA
*
17790 TGTGACAGTGAATAT
1 TGTGACAGTAAATAT
17805 ATTGTAATGA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 74 0.96
73 3 0.04
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (72 bp):
TGTGACAGTAAATATGTGAGTATGTTATTCATGCCATGAGATAGAAAATATATGGGTATATTATT
TATGTCA
Found at i:17804 original size:36 final size:36
Alignment explanation
Indices: 17646--17810 Score: 143
Period size: 36 Copynumber: 4.6 Consensus size: 36
17636 TGATGGCTAT
* * * *
17646 TGTGATAGTAAATGTGTGAGTATGTTATTCATGCCA
1 TGTGACAGTAAATATATGTGTATGTTATTCATGCCA
* * * * * * *
17682 TGGGATAGTAAATATGTGGGTATATTTTTCATGTCA
1 TGTGACAGTAAATATATGTGTATGTTATTCATGCCA
* * *
17718 TGTGACAGTAAATATGTGAGTATGTTATTCATGCCT
1 TGTGACAGTAAATATATGTGTATGTTATTCATGCCA
* * * * *
17754 TGAGATAGAAAATATATGTGTATGTTATTTATGTCA
1 TGTGACAGTAAATATATGTGTATGTTATTCATGCCA
*
17790 TGTGACAGTGAATATAT-TGTA
1 TGTGACAGTAAATATATGTGTA
17811 ATGATGATGT
Statistics
Matches: 104, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
35 4 0.04
36 100 0.96
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (36 bp):
TGTGACAGTAAATATATGTGTATGTTATTCATGCCA
Found at i:21393 original size:24 final size:24
Alignment explanation
Indices: 21361--21406 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
21351 GGAGTAGTTA
21361 TATGCTAGGAACCAGTGAATGTTG
1 TATGCTAGGAACCAGTGAATGTTG
*
21385 TATGCTAGGAACCGGTGAATGT
1 TATGCTAGGAACCAGTGAATGT
21407 AGCAAAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (24 bp):
TATGCTAGGAACCAGTGAATGTTG
Found at i:26383 original size:59 final size:56
Alignment explanation
Indices: 26303--26518 Score: 277
Period size: 49 Copynumber: 3.9 Consensus size: 56
26293 GTGATTAAAT
* * *
26303 GTGATTAATATGTGATGTGATAAATGCTAAAATATTCATGTAATTAAATGTGACAAAA
1 GTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAATGTGAC--AA
26361 TGTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAA--T----A
1 -GTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAATGTGACAA
** *
26412 -TGATTAATATGTGATATGATAAATAATGAAATATTCATGTGATTAAATGTGACTA
1 GTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAATGTGACAA
* *
26467 GTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACT-AATGTGA
1 GTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAATGTGA
26519 TTAATATGTG
Statistics
Matches: 141, Mismatches: 9, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
49 45 0.32
51 2 0.01
55 8 0.06
56 40 0.28
57 1 0.01
59 45 0.32
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (56 bp):
GTGATTAATATGTGATATGATAAATGCTGAAATATTCATGTGATTAAATGTGACAA
Found at i:26440 original size:26 final size:25
Alignment explanation
Indices: 26358--26436 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
26348 AAATGTGACA
*
26358 AAATGTGATTAATATGTGATATGAT
1 AAATATGATTAATATGTGATATGAT
* * *
26383 AAATGCTGA--AATAT-TCATGTGATT
1 AAAT-ATGATTAATATGTGATATGA-T
26407 AAATATGATTAATATGTGATATGAT
1 AAATATGATTAATATGTGATATGAT
26432 AAATA
1 AAATA
26437 ATGAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 9 0.21
24 10 0.23
25 15 0.35
26 9 0.21
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (25 bp):
AAATATGATTAATATGTGATATGAT
Found at i:26472 original size:17 final size:15
Alignment explanation
Indices: 26448--26492 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
26438 TGAAATATTC
26448 ATGTGATTAAATGTG
1 ATGTGATTAAATGTG
26463 ACTAGTGATTAATATGTG
1 A-T-GTGATTAA-ATGTG
26481 ATGTGA-TAAATG
1 ATGTGATTAAATG
26493 CTGAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 5 0.19
17 9 0.33
18 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (15 bp):
ATGTGATTAAATGTG
Found at i:26539 original size:48 final size:48
Alignment explanation
Indices: 26458--26571 Score: 126
Period size: 48 Copynumber: 2.4 Consensus size: 48
26448 ATGTGATTAA
*
26458 ATGTGACT-A-GTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGACTAATGTGATTAATATGTGATGTGATAAATGCTGAAATACTC
* ** *
26504 ATGTGACTAATGTGATTAATATGTGTTGT-ATTAAATTTTTAAATACTC
1 ATGTGACTAATGTGATTAATATGTGATGTGA-TAAATGCTGAAATACTC
* **
26552 ATGTGATTAATACGATTAAT
1 ATGTGACTAATGTGATTAAT
26572 GTGTAAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
46 8 0.14
47 2 0.04
48 47 0.82
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (48 bp):
ATGTGACTAATGTGATTAATATGTGATGTGATAAATGCTGAAATACTC
Found at i:27934 original size:32 final size:32
Alignment explanation
Indices: 27892--27959 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
27882 CTTAATGCGT
27892 TTTTGAATGATTATTTGATGTAAATTGGTTAA
1 TTTTGAATGATTATTTGATGTAAATTGGTTAA
* *
27924 TTTTGGATGATTATTTGATGTAAATTGGTTAC
1 TTTTGAATGATTATTTGATGTAAATTGGTTAA
27956 TTTT
1 TTTT
27960 ATGCTCCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.53
Consensus pattern (32 bp):
TTTTGAATGATTATTTGATGTAAATTGGTTAA
Found at i:29667 original size:20 final size:21
Alignment explanation
Indices: 29578--29683 Score: 133
Period size: 21 Copynumber: 5.1 Consensus size: 21
29568 TAACATGCAG
*
29578 GGGCACCAAAGTGCTATACAA
1 GGGCACCAAAGTGCAATACAA
* *
29599 GGGCACCAAAGTACATTACAA
1 GGGCACCAAAGTGCAATACAA
*
29620 GGGCACCAGAGTGCAATACAA
1 GGGCACCAAAGTGCAATACAA
* * *
29641 AGGCACCGAAGTGCAATA-TA
1 GGGCACCAAAGTGCAATACAA
*
29661 GGGCACCGAAGTGCAATACAA
1 GGGCACCAAAGTGCAATACAA
29682 GG
1 GG
29684 TTTTATTTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 18 0.25
21 54 0.75
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12
Consensus pattern (21 bp):
GGGCACCAAAGTGCAATACAA
Found at i:32028 original size:13 final size:13
Alignment explanation
Indices: 32005--32043 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
31995 AACTGCTATT
*
32005 AACTGACAATAAC
1 AACTAACAATAAC
*
32018 AGCTAACAATAAC
1 AACTAACAATAAC
*
32031 AACTAACACTAAC
1 AACTAACAATAAC
32044 TGTTGATAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.54, C:0.26, G:0.05, T:0.15
Consensus pattern (13 bp):
AACTAACAATAAC
Found at i:42677 original size:23 final size:23
Alignment explanation
Indices: 42619--42680 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
42609 ACCGTGACGT
* *
42619 TATTCGTGTCACGTGTCACAATAT
1 TATTC-TGTCATGTGTCACAATAG
* **
42643 TATTTTACCATGTGTCACAATAG
1 TATTCTGTCATGTGTCACAATAG
42666 TATTCTGTCATGTGT
1 TATTCTGTCATGTGT
42681 TTCAGATTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (23 bp):
TATTCTGTCATGTGTCACAATAG
Found at i:42775 original size:29 final size:29
Alignment explanation
Indices: 42725--42781 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
42715 GAGTGGACGG
*
42725 AAAAAAAGTTTAAGTAATAATCT-GAAAC
1 AAAAAAAATTTAAGTAATAATCTAGAAAC
42753 AAAAAAAATTATAAGT-ATCAATCTAGAAA
1 AAAAAAAATT-TAAGTAAT-AATCTAGAAA
42782 AAGTAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 11 0.44
29 10 0.40
30 4 0.16
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.25
Consensus pattern (29 bp):
AAAAAAAATTTAAGTAATAATCTAGAAAC
Found at i:43367 original size:14 final size:14
Alignment explanation
Indices: 43350--43394 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
43340 CGGTTACAAG
*
43350 TTTAAAATTTGGGT
1 TTTAAAATTTGGGA
*
43364 TTTAACAGTTTGGGA
1 TTTAA-AATTTGGGA
*
43379 TTTAAGATTTGGGA
1 TTTAAAATTTGGGA
43393 TT
1 TT
43395 CGAGTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (14 bp):
TTTAAAATTTGGGA
Found at i:46720 original size:23 final size:23
Alignment explanation
Indices: 46694--46747 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
46684 TTTTTTAGAA
46694 TTTTTAATAATTATTAAT-ATTTT
1 TTTTTAATAATT-TTAATAATTTT
* *
46717 TTTTTTATAATTTTTATAATTTT
1 TTTTTAATAATTTTAATAATTTT
*
46740 GTTTTAAT
1 TTTTTAAT
46748 TTTGCACTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTAATAATTTTAATAATTTT
Found at i:46739 original size:22 final size:23
Alignment explanation
Indices: 46694--46745 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
46684 TTTTTTAGAA
* *
46694 TTTTTAATAATTATTAATATTTT
1 TTTTTTATAATTATTAATAATTT
*
46717 TTTTTTATAATT-TTTATAATTT
1 TTTTTTATAATTATTAATAATTT
*
46739 TGTTTTA
1 TTTTTTA
46746 ATTTTGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTTATAATTATTAATAATTT
Found at i:53858 original size:23 final size:23
Alignment explanation
Indices: 53828--53873 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53818 CGACACCCTT
53828 TACGCTCGAACCAAGTCTCGCGG
1 TACGCTCGAACCAAGTCTCGCGG
53851 TACGCTCGAACCAAGTCTCGCGG
1 TACGCTCGAACCAAGTCTCGCGG
53874 CCTTACCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.26, T:0.17
Consensus pattern (23 bp):
TACGCTCGAACCAAGTCTCGCGG
Found at i:56264 original size:38 final size:38
Alignment explanation
Indices: 56222--56302 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
56212 AGAAATATTT
*
56222 AGCATATACGGTTATATGATACAATTACAACTCATGTG
1 AGCATATACGATTATATGATACAATTACAACTCATGTG
* * *
56260 AGCATATACGATTATATGATACAGTTACAGCTCGTGTG
1 AGCATATACGATTATATGATACAATTACAACTCATGTG
56298 AGCAT
1 AGCAT
56303 TTCTCGAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (38 bp):
AGCATATACGATTATATGATACAATTACAACTCATGTG
Found at i:56633 original size:13 final size:13
Alignment explanation
Indices: 56617--56651 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
56607 AAATGGTAAA
56617 ATGAAATGTTTAG
1 ATGAAATGTTTAG
* *
56630 ATGAAATGGTTAT
1 ATGAAATGTTTAG
56643 ATGAAATGT
1 ATGAAATGT
56652 CTTTATGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (13 bp):
ATGAAATGTTTAG
Found at i:57755 original size:21 final size:21
Alignment explanation
Indices: 57729--57774 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
57719 ACGGTCTAAA
*
57729 CACATGGGCGTGTGGAGTAGC
1 CACATGGGCGTGTGGAGTAAC
* *
57750 CACATGGGTGTGTGGGGTAAC
1 CACATGGGCGTGTGGAGTAAC
57771 CACA
1 CACA
57775 CGACCATGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
CACATGGGCGTGTGGAGTAAC
Found at i:67231 original size:27 final size:27
Alignment explanation
Indices: 67180--67234 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
67170 ATAAAATTAT
* *
67180 GAAATTATAATTAAATATATCAAAAAA
1 GAAATTACAATTAAAAATATCAAAAAA
*
67207 GAAATTACAATTAAAAATTATAAAAAAA
1 GAAATTACAATTAAAAA-TATCAAAAAA
67235 TGTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (27 bp):
GAAATTACAATTAAAAATATCAAAAAA
Found at i:68186 original size:30 final size:30
Alignment explanation
Indices: 68150--68208 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
68140 ACTTATTGTT
68150 AATATTT-TAA-TATATGAAATATTAATTTTA
1 AATATTTCTAAGTA-AT-AAATATTAATTTTA
*
68180 AATATTTCTAAGTAATTAATATTAATTTT
1 AATATTTCTAAGTAATAAATATTAATTTT
68209 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 19 0.73
31 5 0.19
32 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
AATATTTCTAAGTAATAAATATTAATTTTA
Found at i:68818 original size:4 final size:4
Alignment explanation
Indices: 68805--68847 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
68795 AAAATTGAAG
* *
68805 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA TAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
68848 GAAGGAGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:69263 original size:20 final size:21
Alignment explanation
Indices: 69222--69264 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
69212 TAATTTACTT
69222 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
69243 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
69263 TA
1 TA
69265 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.